Agatha Heterodyne and the Monster Engine by Phil and Kaja Folgio.  Volume 3 of Agatha Heterodyne, Girl Genius!

Another chapter in the story (she repeats from the first two, like an automated recording), with spoilers for the first two.  But this one is a definite end of the beginning.  The opening questions are clarified here, to end with a sharp turn.

Gil does, as promised last time, take on Agatha as a lab assistant. His father the Baron goes to perform an experiment on a prisoner, to remove his Spark. And a secretive mole starts trouble.

Action, adventure, explosions! Daring rescues! Bravely fencing the way to the heart of the problem! Bangladesh Dupree, the Baron's psychotic pirate henchwoman! An inept and rather abrupt marriage proposal! And then revelation after revelation!

You know, reading with the benefit of hindsight lets in a lot of details. Like exactly what Agatha was doing when Bang saw her.